Research workbench
Crystal structure of dxr from thermotoga maritima, in complex with NADPH
Analyse Crystal structure of dxr from thermotoga maritima, in complex with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A14
- Type
- protein
- Length
- 729 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase
- EC
- 1.1.1.267
- UniProt
- Q9WZZ1
- Ligands
- NDP, MG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 362 | 47% helix, 17% strand | Q9WZZ1 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 367 | 47% helix, 16% strand | Q9WZZ1 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.72 | 0.80 | 60 | NDP, MG, MPD |
| 2 | 584 | 0.69 | 0.78 | 73 | NDP, MG, MPD |
| 3 | 75 | 0.36 | 0.76 | 13 | empty |
| 4 | 59 | 0.34 | 0.78 | 13 | empty |
| 5 | 64 | 0.34 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1885 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3A14 · Crystal structure of DXR from Thermotoga maritima, in complex with NADPH · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZZ1 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9WZZ1
- Elsewhere: RCSB PDB 3A14 · PDBe 3A14 · UniProt Q9WZZ1
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